Search

Soil salinity has a major impact on rice seed germination, severely limiting rice production. Herein, a rice germination defective mutant under salt stress (gdss) was identified by using chemical mutagenesis. The GDSS gene was detected via MutMap and shown to encode potassium transporter OsHAK9. Phenotypic analysis of complementation and mutant lines demonstrated that OsHAK9 was an essential regulator responsible for seed germination under salt stress. OsHAK9 is highly expressed in germinating seed embryos. Ion contents and non‐invasive micro‐test technology results showed that OsHAK9 restricted K+ efflux in salt‐exposed germinating seeds for the balance of K+/Na+. Disruption of OsHAK9 significantly reduced gibberellin 4 (GA4) levels, and the germination defective phenotype of oshak9a was partly rescued by exogenous GA3 treatment under salt stress. RNA sequencing (RNA‐seq) and real‐time quantitative polymerase chain reaction analysis demonstrated that the disruption of OsHAK9 improved the GA‐deactivated gene OsGA2ox7 expression in germinating seeds under salt stress, and the expression of OsGA2ox7 was significantly inhibited by salt stress. Null mutants of OsGA2ox7 created using clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR‐associated nuclease 9 approach displayed a dramatically increased seed germination ability under salt stress. Overall, our results highlight that OsHAK9 regulates seed germination performance under salt stress involving preventing GA degradation by mediating OsGA2ox7, which provides a novel clue about the relationship between GA and OsHAKs in rice. [ABSTRACT FROM AUTHOR]

Rice blast is one of the most devastating diseases, causing a significant reduction in global rice production. Developing and utilizing resistant varieties has proven to be the most efficient and cost-effective approach to control blasts. However, due to environmental pressure and intense pathogenic selection, resistance has rapidly broken down, and more durable resistance genes are being discovered. In this paper, a novel wall-associated kinase (WAK) gene, Pb4, which confers resistance to rice blast, was identified through a genome-wide association study (GWAS) utilizing 249 rice accessions. Pb4 comprises an N-terminal signal peptide, extracellular GUB domain, EGF domain, EGF-Ca2+ domain, and intracellular Ser/Thr protein kinase domain. The extracellular domain (GUB domain, EGF domain, and EGF-Ca2+ domain) of Pb4 can interact with the extracellular domain of CEBiP. Additionally, its expression is induced by chitin and polygalacturonic acid. Furthermore, transgenic plants overexpressing Pb4 enhance resistance to rice blast. In summary, this study identified a novel rice blast-resistant gene, Pb4, and provides a theoretical basis for understanding the role of WAKs in mediating rice resistance against rice blast disease. [ABSTRACT FROM AUTHOR]

Non-coding RNAs (ncRNAs) play important roles in regulating expression of protein-coding genes. Although gene expression databases have emerged in a timely manner, a comprehensive expression database for ncRNAs is still lacking. Herein, we constructed a rice ncRNA co-expression atlas (RiceNCexp), based on 491 RNA-seq and 274 small RNA (sRNA)-seq datasets. RiceNCexp hosts four types of ncRNAs, namely lncRNAs, PHAS genes, miRNAs, and phasiRNAs. RiceNCexp provides comprehensive expression information for rice ncRNAs in 22 tissues/organs, an efficient tau-based mining tool for tissue-specific ncRNAs, and the robust co-expression analysis among ncRNAs or between ncRNAs and protein-coding genes, based on 116 pairs of RNA-seq and sRNA-seq libraries from the same experiments. In summary, RiceNCexp is a user-friendly and comprehensive rice ncRNA co-expression atlas and can be freely accessed at https://cbi.njau.edu.cn/RiceNCexp/. [ABSTRACT FROM AUTHOR]

Drought stress is one of the major environmental factors affecting crop growth and productivity. Cuticular wax plays essential roles in protecting plants from environmental stress via forming a hydrophobic barrier on leaf epidermis. In this study, we analyzed nine members (OsCUT1‒OsCUT9) of β-ketoacyl-CoA synthase, the rate-limiting key enzyme for cuticular wax synthesis in rice by homology search and domain prediction. The expression levels of OsCUT genes under different abiotic stresses were investigated and OsCUT1 down-regulated by abiotic stress was selected for further function validation. Compared to the wild type, overexpression of OsCUT1 (OX-OsCUT1) exhibited significantly increased drought resistance. Epicuticular wax was increased on the leaf surface of OX-OsCUT1 and the chlorophyll leaching experiment showed that the cuticular permeability was decreased in the OX-OsCUT1 plants. Moreover, overexpression of OsCUT1 didn't result in the significant changes of major agronomic traits. In total, these results suggested that OsCUT1 is a promising gene for engineering rice plants with enhanced drought tolerance. [ABSTRACT FROM AUTHOR]

Summary: The cultivation of rice varieties with high seed vigour is vital for the direct seeding of rice, and the molecular basis of regulation of seed vigour remains elusive. Here, we cloned a new gene OsHIPL1, which encodes hedgehog‐interacting protein‐like 1 protein as a causal gene of the major QTL qSV3 for rice seed vigour. OsHIPL1 was mainly localized in the plasma membrane and nucleus. RNA sequencing (RNA‐seq) revealed that the ABA‐related genes were involved in the OsHIPL1 regulation of seed vigour in rice. The higher levels of endogenous ABA were measured in germinating seeds of OsHIPL1 mutants and NIL‐qsv3 line compared to IR26 plants, with two up‐regulated ABA biosynthesis genes (OsZEP and OsNCED4) and one down‐regulated ABA catabolism gene OsABA8ox3. The expression of abscisic acid‐insensitive 3 (OsABI3), OsABI4 and OsABI5 was significantly up‐regulated in germinating seeds of OsHIPL1 mutants and NIL‐qsv3 line compared to IR26 plants. These results indicate that the regulation of seed vigour of OsHIPL1 may be through modulating endogenous ABA levels and altering OsABIs expression during seed germination in rice. Meanwhile, we found that OsHIPL1 interacted with the aquaporin OsPIP1;1, then affected water uptake to promote rice seed germination. Based on analysis of single‐nucleotide polymorphism data of rice accessions, we identified a Hap1 haplotype of OsHIPL1 that was positively correlated with seed germination. Our findings showed novel insights into the molecular mechanism of OsHIPL1 on seed vigour. [ABSTRACT FROM AUTHOR]

Seed germination plays a pivotal role in the plant life cycle, and its precise regulatory mechanisms are not clear. In this study, 19 quantitative trait loci (QTLs) associated with rice seed germination were identified through genome-wide association studies (GWAS) of the following traits in 2016 and 2017: germination rate (GR) at 3, 5, and 7 days after imbibition (DAI) and germination index (GI). Two major stable QTLs, qSG4 and qSG11.1 , were found to be associated with GR and GI over 2 continuous years. Furthermore, OsPK5 , encoding a pyruvate kinase, was shown to be a crucial regulator of seed germination in rice, and might be a causal gene of the key QTL qSG11.1 , on chromosome 11. Natural variation in OsPK5 function altered the activity of pyruvate kinase. The disruption of OsPK5 function resulted in slow germination and seedling growth during seed germination, blocked glycolytic metabolism, caused glucose accumulation, decreased energy levels, and affected the GA/ABA balance. Taken together, our results provide novel insights into the roles of OsPK5 in seed germination, and facilitate its application in rice breeding to improve seed vigour. [ABSTRACT FROM AUTHOR]

Rice blast is one of the main diseases in rice and can occur in different rice growth stages. Due to the complicated procedure of panicle blast identification and instability of panicle blast infection influenced by the environment, most cloned rice resistance genes are associated with leaf blast. In this study, a rice panicle blast resistance gene, Pb2, was identified by genome-wide association mapping based on the panicle blast resistance phenotypes of 230 Rice Diversity Panel 1 (RDP1) accessions with 700,000 single-nucleotide polymorphism (SNP) markers. A genome-wide association study identified 18 panicle blast resistance loci (PBRL) within two years, including 9 reported loci and 2 repeated loci (PBRL2 and PBRL13, PBRL10 and PBRL18). Among them, the repeated locus (PBRL10 and PBRL18) was located in chromosome 11. By haplotype and expression analysis, one of the Nucleotide-binding domain and Leucine-rich Repeat (NLR) Pb2 genes was highly conserved in multiple resistant rice cultivars, and its expression was significantly upregulated after rice blast infection. Pb2 encodes a typical NBS-LRR protein with NB-ARC domain and LRR domain. Compared with wild type plants, the transgenic rice of Pb2 showed enhanced resistance to panicle and leaf blast with reduced lesion number. Subcellular localization of Pb2 showed that it is located on plasma membrane, and GUS tissue-staining observation found that Pb2 is highly expressed in grains, leaf tips and stem nodes. The Pb2 transgenic plants showed no difference in agronomic traits with wild type plants. It indicated that Pb2 could be useful for breeding of rice blast resistance. [ABSTRACT FROM AUTHOR]

SUMMARY: Oryza sativa L. (rice) is one of the most important crops in the world, and grain size is a major component determining rice yield. Recent studies have identified a number of grain size regulators, which are involved in phytohormone signaling, G protein signaling, the mitogen‐activated protein kinase signaling pathway, the ubiquitin–proteasome pathway or transcriptional regulation. In a previous study, we cloned qGL3/OsPPKL1 encoding a rice protein phosphatase that negatively modulates brassinosteroid (BR) signaling and grain length. Here, to further explore the qGL3‐mediated BR signaling network, we performed phosphoproteomic screenings using two pairs of rice materials: the indica rice cultivar 9311 and its near‐isogenic line NILqgl3 and the japonica rice cultivar Dongjin and its qGL3 knockout mutant m‐qgl3. Together with qGL3‐interacting proteins, we constructed the qGL3‐mediated network, which reveals the relationships between BR signaling and other critical signaling pathways. Transgenic plants of these network components showed BR‐related alterations in plant architecture. From this network, we validated a qGL3‐interacting protein, O. sativa VERNALIZATION INSENSITIVE 3‐LIKE 1 (OsVIL1), and demonstrated that qGL3 dephosphorylates OsVIL1 to modulate BR signaling. The qGL3‐dependent network uncovered in this study increases our understanding of BR signaling and provides a profound foundation for addressing how BR modulates plant architecture in rice. Significance Statement: To enrich the rice brassinosteroid (BR) signaling pathway, the qGL3‐dependent network was constructed with phosphoproteomic and interactomic data. [ABSTRACT FROM AUTHOR]

Background: Grain size is one of the major determinants of cereal crop yield. As a class of plant polyhydroxysteroids, brassinosteroids (BRs) play essential roles in the regulation of grain size and plant architecture in rice. In a previous research, we cloned qGL3/OsPPKL1 encoding a protein phosphatase with Kelch-like repeat domains, which negatively regulates BR signaling and grain length in rice. Results: Here, we screened qGL3-interacting proteins (GIPs) via yeast two-hybrid assay and analyzed the phenotypes of the T-DNA insertion mutants of GIPs. Among these mutants, mutant osak3 presents shorter grain length and dwarfing phenotype. OsAK3 encodes an adenylate kinase, which regulates grain size by controlling cell expansion of rice spikelet glume. Overexpression of OsAK3 resulted in longer grain length. OsAK3 interacts with qGL3 in vivo and in vitro. Lamina inclination, coleoptile elongation and root inhibition experiments showed that the osak3 mutant was less sensitive to exogenous brassinolide (BL) treatment. The transcriptional level of OsAK3 was up-regulated under BL induction. In addition, RNA-Seq data indicate that OsAK3 is involved in a variety of biological processes that regulate BR signaling and grain development in rice. Conclusions: Our study reveals a novel BR signaling component OsAK3 in the regulation of grain length, and provides novel clues for uncovering the potential functions of OsAK3 in rice growth and development. [ABSTRACT FROM AUTHOR]

Summary: The plant Shaker K+ channel AtAKT2 has been identified as a weakly rectifying channel that can stabilize membrane potentials to promote photoassimilate phloem loading and translocation. Thus, studies on functional characterization and regulatory mechanisms of AtAKT2‐like channels in crops are highly important for improving crop production. Here, we identified the rice OsAKT2 as the ortholog of Arabidopsis AtAKT2, which is primarily expressed in the shoot phloem and localized at the plasma membrane. Using an electrophysiological assay, we found that OsAKT2 operated as a weakly rectifying K+ channel, preventing H+/sucrose‐symport‐induced membrane depolarization. Three critical amino acid residues (K193, N206, and S326) are essential to the phosphorylation‐mediated gating change of OsAKT2, consistent with the roles of the corresponding sites in AtAKT2. Disruption of OsAKT2 results in delayed growth of rice seedlings under short‐day conditions. Interestingly, the lipid second messenger phosphatidic acid (PA) inhibits OsAKT2‐mediated currents (both instantaneous and time‐dependent components). Lipid dot‐blot assay and liposome‐protein binding analysis revealed that PA directly bound with two adjacent arginine residues in the ANK domain of OsAKT2, which is essential to PA‐mediated inhibition of OsAKT2. Electrophysiological and phenotypic analyses also showed the PA‐mediated inhibition of AtAKT2 and the negative correlation between intrinsic PA level and Arabidopsis growth, suggesting that PA may inhibit AKT2 function to affect plant growth and development. Our results functionally characterize the Shaker K+ channel OsAKT2 and reveal a direct link between phospholipid signaling and plant K+ channel modulation. Significance Statement: Phospholipids function as second messengers, modulating some kinds of ion channels in animal cells, but in plants, phospholipid‐mediated modulation of ion channels remains unclear. Herein, we identified OsAKT2 (a Shaker family member in rice) as a weakly rectifying K+ channel and found that phosphatidic acid, a lipid mediator, inhibited OsAKT2 activity by binding with two adjacent arginine residues in the ANK domain, revealing a direct link between phospholipid signaling and plant K+ channel modulation. [ABSTRACT FROM AUTHOR]

Summary: Seed germination is a complex trait determined by both quantitative trait loci (QTLs) and environmental factors and also their interactions. In this study, we mapped one major QTLqSE3 for seed germination and seedling establishment under salinity stress in rice. To understand the molecular basis of this QTL, we isolated qSE3 by map‐based cloning and found that it encodes a K+ transporter gene, OsHAK21. The expression of qSE3 was significantly upregulated by salinity stress in germinating seeds. Physiological analysis suggested that qSE3 significantly increased K+ and Na+ uptake in germinating seeds under salinity stress, resulting in increased abscisic acid (ABA) biosynthesis and activated ABA signaling responses. Furthermore, qSE3 significantly decreased the H2O2 level in germinating seeds under salinity stress. All of these seed physiological changes modulated by qSE3 might contribute to seed germination and seedling establishment under salinity stress. Based on analysis of single‐nucleotide polymorphism data of rice accessions, we identified a HAP3 haplotype of qSE3 that was positively correlated with seed germination under salinity stress. This study provides important insights into the roles of qSE3 in seed germination and seedling establishment under salinity stress and facilitates the practical use of qSE3 in rice breeding. Significance Statement: One major QTL qSE3 for rice seed germination and seedling establishment under salinity stress was map‐based cloned, which promotes seed germination under salinity stress by enhancing K+ and Na+ uptake, increasing ABA biosynthesis and ABA signaling responses and reducing H2O2 levels in germinating seeds. The application of qSE3 might be useful for improving salinity tolerance and breeding varieties suitable for direct seeding in rice. [ABSTRACT FROM AUTHOR]

Phased small interfering RNAs (phasiRNAs) are a class of non-coding RNAs that perform essential functions in plants. Unlike microRNA biogenesis from a hairpin structure, the production of phasiRNAs usually requires a phase initiator and an RNA-dependent RNA polymerase (RDR) to form double-strand RNAs. By using full-length rice cDNA (KL-cDNA) to identify phasiRNA loci, we found that a putative non-coding sequence with a long hairpin structure generates the phasiRNAs, which we name Long Hairpin-structure containing non-coding RNA (LHR). The biogenesis of LHR -derived phasiRNAs was dependent on rice DCL4, but not on RDR2/6, DCL1, or DCL3. Since all of the LHR -phasiRNAs (-5p from the forward strand and -3p from the reverse strand of the dsRNAs) are mapped to the forward strand of LHR, LHR -phasiRNAs should be derived from its hairpin structure, similar to a microRNA precursor. A degradome-based validation suggested that several thylakoid-related genes were targeted by LHR -phasiRNAs. In addition, the production of LHR -phasiRNAs was completely abolished in the lhr mutant, which also exhibited decreased plant height, leaf size, and grain weight, probably through the regulation of photosynthesis. Based on our results, we propose a microRNA biogenesis-like pathway for producing phased siRNAs that expands our understanding of the current model of phased siRNA biogenesis in plants. [ABSTRACT FROM AUTHOR]

The C2H2-type zinc finger proteins (ZFPs) are involved in a wide range of plant development and stress responses. Many studies have shown the positive roles of ZFP genes in stress tolerance. However, overexpression of ZFP genes usually leads to the side effect of growth retardation. Here we report a new member of the ZFP family, Oryza sativa drought-responsive zinc finger protein 1 (OsDRZ1), positively regulating both stress tolerance and plant architecture in rice (Oryza sativa L.). OsDRZ1 was expressed throughout all tissues examined and could be induced by multiple abiotic stresses. OsDRZ1 protein was localized mostly in the nucleus. Unlike most reported rice ZFPs functioning as transcriptional activators, OsDRZ1 is a transcriptional repressor. Overexpression of OsDRZ1 in rice increased seedling drought tolerance and the transgenic plants appeared to accumulate more free proline and fewer reactive oxygen species (ROS), and elevate the activities of antioxidant enzymes. In contrast, RNA interference (RNAi) of OsDRZ1 led to lower activities of antioxidative response and more sensitivity to drought. RNA sequencing analysis revealed that the genes down-regulated by OsDRZ1 were mostly down-regulated by drought, implying the critical role of OsDRZ1 in modulating drought-responsive gene expression. A cupin gene OsGLP1 (germin-like protein1) was identified as one of the potential target genes of OsDRZ1, as suggested by real-time PCR and transient expression analysis in rice protoplasts. Moreover, overexpression of OsDRZ1 did not lead to growth inhibition but the promotion of rice growth, implying the potential application prospective of OsDRZ1 in engineering drought-tolerant crops. [ABSTRACT FROM AUTHOR]

Rice blast is a destructive disease caused by Magnaporthe oryzae, and it has a large impact on rice production worldwide. Compared with leaf blast resistance, our understanding of panicle blast resistance is limited. The japonica landrace Jiangnanwan from Taihu Lake region in China shows highly resistance to panicle and leaf blast. In this study, three generations (F2:5, F2:6, F2:7) consisting of 221 RILs (recombination inbreeding lines), developed from the cross of Jiangnanwan and Suyunuo, a susceptible-blast japonica variety, were evaluated for panicle blast resistance in the fields and leaf blast resistance in greenhouse in Nanjing in 2013, 2014 and 2015. A blast resistance gene Pi-jnw1 referring to panicle blast resistance and leaf blast resistance was identified in the three generations and located in the region of RM27273 and RM27381 in chromosome 11. The RIL18 line harboring Pi-jnw1 was selected to be backcrossed with Suyunuo to develop BC2F2 populations. According to the genotyping of 1,150 BC2F2 individuals and panicle blast and leaf blast resistance evaluation of 47 recombinants between RM27150 and RM27381, Pi-jnw1 was finally mapped to the 282 kb region between markers W28 and BS39. This study revealed that Jiangnanwan harboring a panicle blast and leaf blast resistance gene Pi-jnw1 could be a genetic source for breeding new rice cultivars with panicle blast resistance. [ABSTRACT FROM AUTHOR]

Copyright of Botany is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Salt stress is one of most serious limiting factors for crop growth and production. An isobaric Tags for Relative and Absolute Quantitation (iTRAQ) approach was used to analyze proteomic changes in rice shoots under salt stress in this study. A total of 56 proteins were significantly altered and 16 of them were enriched in the pathways of photosynthesis, antioxidant and oxidative phosphorylation. Among these 16 proteins, peroxiredoxin Q and photosystem I subunit D were up-regulated, while thioredoxin M-like, thioredoxin x, thioredoxin peroxidase, glutathione S-transferase F3, PSI subunit H, light-harvesting antenna complex I subunits, chloroplast chaperonin, vacuolar ATP synthase subunit H, and ATP synthase delta chain were down-regulated. Moreover, physiological data including total antioxidant capacity, peroxiredoxin activity, chlorophyll a/b content, glutathione S-transferase activity, reduced glutathione content and ATPase activity were consistent with changes in the levels of these proteins. The levels of the mRNAs encoding these proteins were also analyzed by real-time quantitative reverse transcription PCR, and approximately 86% of the results were consistent with the iTRAQ data. Importantly, our data suggest the important role of PSI in balancing energy supply and ROS generation under salt stress. This study provides information for an improved understanding of the function of photosynthesis and PSI in the salt-stress response of rice. [ABSTRACT FROM AUTHOR]

To study tolerance of rice (Oryza sativa L.) to excessive copper (Cu), 167 varieties were screened for Cu tolerance or sensitivity. Based on the elongation of the root, No. 1139 and No. 1195 were chosen as Cu-tolerant and Cu-sensitive variety. Compared with the control (0.32 μ mol L- 1 Cu), treatments with 5 and 8 μ mol L- 1 Cu for 10 days had no significant effect on the root and shoot dry masses of Cu-tolerant variety No. 1139, but significantly decreased root and shoot dry masses of variety No. 1195. Copper at 5 and 8 μ mol L- 1 also significantly decreased contents of chlorophyll and carotenoid and the ratio of variable to maximal chlorophyll fluorescence (Fv/Fm) in the leaves of the Cu-sensitive variety No. 1195. Roots and shoots of variety No. 1139 contained significantly higher the concentration of Cu than variety No. 1195 exposed to 5 and 8 μ mol L- 1 Cu. However, variety No. 1139 had higher Cu proportions on the cell walls in shoots and roots than variety No. 1195. [ABSTRACT FROM AUTHOR]

• OsPDR1 positively regulates JAs contents, cell death and pathogen resistance. • OsPDR1 is involved in fine-tuning of plant growth and development. • Three OsPDR1 isoforms play distinct roles in rice plants. Jasmonates (JAs) are important regulators of plant growth, development, and defense. ATP-binding cassette (ABC) transporters participate in disease resistance by transporting JAs or antimicrobial secondary metabolites in dicotyledons. Here, we functionally characterized a JAs-inducible rice gene (OsPDR1) that encodes a member of the pleiotropic drug resistance (PDR) subfamily of ABC transporters. By affecting JAs biosynthesis, overexpression of OsPDR1 resulted in constitutive activation of defense-related genes and enhanced resistance to bacterial blight, whereas its mutation decreased pathogen resistance. In addition, overexpression and mutation of OsPDR1 resulted in decreased and increased plant growth at seedling stage, respectively, but eventually led to decreased grain yield. OsPDR1 encodes three splice isoforms, of which OsPDR1.2 and OsPDR1.3 contain a conserved glutamate residue in the "ENI-motif" of the first nucleotide-binding domain, while OsPDR1.1 does not. The three OsPDR1 transcripts are developmentally controlled and differentially regulated by JAs and pathogen infection. The OsPDR1.2 - and OsPDR1.3 -overexpressing plants exhibited higher JAs content and stronger growth inhibition and disease resistance than OsPDR1.1 -overexpressing plants. These results indicated that alternative splicing affects the function of OsPDR1 gene in regulation of growth, development and disease resistance. [ABSTRACT FROM AUTHOR]

Background: Rice (Oryza sativa L.) yield is seriously influenced by panicle exsertion (PE) and the uppermost internode (UI) through panicle enclosure or energy transport during grain-filling stages. We evaluated the traits of PE and UI of 205 rice accessions in two independent environments and performed genome-wide association (GWAS) to explore the key genes controlling PE and UI, which could be used to improve panicle enclosure in rice breeding. Results: In this study, extensive genetic variation was found in both PE and UI among the 205 rice accessions, and 10.7% of accessions had panicle enclosure (PE/UI ≤ 0). Correlation analysis revealed that PE was significantly positively correlated with 1000-grain weight (1000-GW) but negatively correlated with heading date (HD), and UI was significantly positively correlated with HD but no significantly correlated with 1000-GW. A total of 22 and 24 quantitative trait loci (QTLs) were identified for PE and UI using GWAS, respectively. Eight loci for PE and nine loci for UI were simultaneously detected both in 2015 and in 2016, seven loci had adjacent physical positions between PE and UI, and ten loci for PE and seven loci for UI were located in previously reported QTLs. Further, we identified the CYP734A4 gene, encoding a cytochrome P450 monooxygenase, and the OsLIS-L1 gene, encoding a lissencephaly type-1-like protein, as causal genes for qPE14 and qUI14, and for qPE19, respectively. PE and UI were both significantly shorter in these two genes' mutants than in WT. Allelic Hap.1/2/4 of CYP734A4 and Hap.1/2/4 of OsLIS-L1 increased PE, UI, PE/UI, and 1000-GW, but Hap.3 of CYP734A4 and Hap.3 of OsLIS-L1 reduced them. In addition, six candidate genes were also detected for four key novel loci, qPE16, qPE21, qUI1, and qUI18, that seemed to be related to PE and UI. Conclusions: Our results provide new information on the genetic architecture of PE and UI in rice, confirming that the CYP734A4 and OsLIS-L1 genes participate in PE and UI regulation, which could improve our understanding of the regulatory mechanism of PE and UI for rice breeding in the future. [ABSTRACT FROM AUTHOR]

Methionine sulfoxide reductases (MSRs), a family of enzymes catalyzing the conversion of methionine from its oxidized form into its reduced form, has a pivotal role in responding to oxidative stress. In the present study, we found that OsMSRB5 plays a crucial role in rice adaption to Cu stress. OsMSRB5 was mainly expressed in leaves, with low transcriptional levels of OsMSRB5 observed in seeds, stems, and roots; this gene was also induced by the excess copper (Cu) treatment. The functions of OsMSRB5 were analyzed through ectopic expression in Escherichia coli and functional disruption in rice. An in vitro enzymatic activity assay showed that OsMSRB5 had the ability to reduce free methionine- R -sulfoxide (Met- R -SO) and protein-bound-like Met-SO (dabsyl-Met-SO) to Met and dabsyl-Met, respectively. Ectopic expression of OsMSRB5 conferred E. coli cells higher tolerance to excess Cu and methyl viologen (MV). Furthermore, OsMSRB5 mutation decreased Cu and MV tolerance in rice. Our results demonstrate that rice OsMSRB5 is a functional methionine sulfoxide reductase and is involved in defense against Cu toxicity. In addition, rice seedlings responding to MV-induced oxidative stress showed a similar phenotype with excess Cu. [ABSTRACT FROM AUTHOR]

Abstract: ZFP245 is a cold- and drought-responsive gene that encodes a zinc finger protein in rice. The ZFP245 protein localizes in the nucleus and exhibits trans-activation activity. Transgenic rice plants overexpressing ZFP245 were generated and found to display high tolerance to cold and drought stresses. The transgenic plants did not exhibit growth retardation, but showed growth sensitivity against exogenous abscisic acid, increased free proline levels and elevated expression of rice pyrroline-5-carboxylatesynthetase and proline transporter genes under stress conditions. Overproduction of ZFP245 enhanced the activities of reactive oxygen species-scavenging enzymes under stress conditions and increased the tolerance of rice seedlings to oxidative stress. Our data suggest that ZFP245 may contribute to the tolerance of rice plants to cold and drought stresses by regulating proline levels and reactive oxygen species-scavenging activities, and therefore may be useful for developing transgenic crops with enhanced tolerance to abiotic stress. [Copyright &y& Elsevier]

Abstract: Calcium plays a crucial role as a second messenger in mediating various defense responses under environmental stresses. Calcineurin B-like (CBL) proteins have been implicated as important Ca2+ sensors in plant-specific calcium signaling. Based on the similarity of sequence, ten CBL genes were identified by searching the rice japonica genome database, which were randomly distribute on chromosomes 1, 2, 3, 5, 10 and 12. By semi-quantitative RT-PCR approach the expression pattern of each gene was detected in various organs at the adult stage and seedlings treated with NaCl, PEG and cold stresses or exogenous ABA. The results showed that the induction of each rice CBL gene was not only responsive to different stress conditions, but also organ specific. In vivo targeting experiment revealed that OsCBL8 localized to the plasma membrane, which was consistent with OsCBL4 and SOS3 previously reported. To elucidate the putative function of OsCBL8 gene, transgenic rice plants overexpressing OsCBL8 gene were generated by the Agrobacterium-mediated approach. The OsCBL8 transgenic rice seedlings showed more tolerance to salt stress than non-transgenic seedlings. [Copyright &y& Elsevier]

• Based on public salt –related microArray data, small RNA-seq and degradome sequence, we constructed and compared salt-response networks in rice and Arabidopsis, consisting of miRNAs, genes and transcription factors (TFs). • In rice, more target genes of networks were enriched in development and growth, while more stress directly-related genes were detected in Arabidopsis networks. • Salt response networks of Arabidopsis are typically organized. • Salt-response mechanisms of rice are emphasized on avoiding salt stress by regulating growth and development according to rice miRNA-TF-genes networks. • MiRNA171-GRAS and miRNA169-NFYA are possible species-conserved salt-response patterns. Not only are they detected in our results, but also reported in other signaling pathways. For instance, miRNA169-NFYA is found work in ABA signaling pathways. By using the available expression datasets of mRNAs and small RNAs, we constructed and compared the salt-responsive gene regulatory networks (GRNs) involving both transcriptional and post-transcriptional regulations between model plants rice and Arabidopsis. The salt-responsive GRNs involve the transcription factors (TFs), microRNAs (miRNAs) and their target genes. Here we describe 552 miRNA-target interactions (MTIs), 95 up-regulated TF-target interactions (TTIs) and 56 down-regulated TTIs in rice, while 332 MTIs, 138 up-regulated and 4 down-regulated TTIs in Arabidopsis. Interestingly, we observed the networks in rice are more complicated where target genes were enriched in rice development and growth, while more stress-related genes were detected in Arabidopsis networks. With the construction and comparison of GRNs between rice and Arabidopsis in response to salt stress, we can basically describe the differences of salt responsive mechanisms in two species: rice tends to respond slower and chooses to manipulate its development and growth to avoid salt stress, while Arabidopsis prefers to trigger a serious salt-defending genes to protect itself from stress. Our work provides the foundation for further exploring the molecular basis of plant salt response and the potential breeding practice by engineering the critical components in the networks in improving plant salt tolerance. [ABSTRACT FROM AUTHOR]

Cytosine DNA methylation (5mC) is an epigenetic mark that regulates gene expression in plant responses to environmental stresses. Zinc-finger protein (ZFP) is the largest family of DNA-binding transcription factors that also plays an essential role in eukaryote. In plant we have already identified and characterized different useful ZFP-genes. While, the main objective of this research was to observe and identify more targeted stress responsive genes of ZFPs epigenetically throughout genome in rice for the first time. A comprehensive correlation analysis was performed through methylated DNA immunoprecipitation (MeDIP)-chip hybridization in rice under salt and osmotic stresses. High salinity and drought are two major abiotic hazards that are destroying the crop world-wide. As a result, Through-out genome 14 unique stress responsive transcription factors of ZFP-genes with varying level of methylation and expression under two conditions (control vs. stress) were isolated. All the identified genes were confirmed from different databases for their specific structure, cis-regulatory elements, phylogenetic analysis, and synteny analysis. Moreover, the tissue-specific expression patterns, and expression under abiotic and phytohormones stresses were also investigated. Phylogenetically all the genes were divided into 6 distinct subgroups with Arabidopsis and orthologous proteins were find-out through synteny analysis. Available RNA-seq data in response to various phytohormones provided hormone inducible gene expression profile. Through Reverse Transcriptase qPCR (RT-qPCR) analysis tissue-specific expression in shoot and root over various time points against salt and osmotic stresses exhibited the diverse expression patterns of identified genes. Overall, the present study providing a foundation for in-depth characterization of identified genes and to further understand the epigenetic role of DNA methylation for genes expression and environmental stresses regulation in higher plant. • 14 unique OsZFP genes partially or fully methylated were identified through MeDIP-chip. • All OsZFPs were clustered in three clades. • RNA-seq data in response to various phytohormones provided hormone specific genes expression profiles. • The candidate rice ZFP genes exhibited diverse expression patterns under salinity and drought stresses. [ABSTRACT FROM AUTHOR]